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In that link, it shows biographies for the characters. I have gleaned the information that, and I quote, Alt. Doof was "molded into a dictator by a single traumatic childhood event.
Also, here's 2nd Dimension Buford's biography:
"He used to be in the Resistance, but he got so good at it, he started resisting them."
That could be the missing link to my theory! I believe that Alt. Doof mind-controlled everyone, after Alt. Buford turned them in!
Danville 11:40, June 19, 2011 (UTC)